Recently we've upgraded Jenkins to v2.32.2 and all SCM / Branch API 2.x related plugins to the following versions:

• cloudbees-bitbucket-branch-source 2.1.0
• branch-api 2.0.6
• cloudbees-folder 5.17
• scm-api 2.0.4
• git 3.0.5
• workflow-multibranch 2.12

Since then multibranch pipeline projects tend to mark specific branches (mostly develop) as dead after processing events from the following endpoint (from Scan Multibranch Pipeline Events log):

[Thu Feb 16 08:47:22 CET 2017] jenkins.plugins.git.GitSCMSource$ListenerImpl$1 UPDATED event from <Bitbucket Server IP> ⇒ <Jenkins Host>:<random port>/git/notifyCommit with timestamp Thu Feb 16 08:47:20 CET 2017 processed in 1.6 sec

Such events happen when any other non-multibranch-pipeline jobs get triggered by a Bitbucket Server webhook on the /git/notifyCommit endpoint published by the Git plugin. I guess the bitbucket-branch-source-plugin listens to these events but cannot interpret their payload correctly.

SCM environment:

• Bitbucket Server v4.10.1
• Webhook to Jenkins for Bitbucket v3.0.1
• (We use the preferred Post Webhooks for Bitbucket v1.2.0 to trigger multibranch-pipeline jobs)

After the triggered non-multibranch pipeline job finishes dead branches immediately appear in all of the Bitbucket Team/Project folders.